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Sample GSM1431037 Query DataSets for GSM1431037
Status Public on Mar 01, 2015
Title P1805N
Sample type genomic
Source name Serous ovarian tumor
Organism Homo sapiens
Characteristics tissue: Peripheral Blood Lymphocytes
tumour histology: SEROUS
somatic ras/raf mutations: WT
age at diagnosis: Unknown
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from tissues (epithelium and stroma) microdissected mucinous ovarian tumours stained with haematoxylin and eosin, and from lymphcoytes obtained from peripheral blood (for matched normal DNA) using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and Qubit.
Label protocol As per manufacturer's recommendations (Affymetrix)
Hybridization protocol DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.
Scan protocol The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.
Description HYBRIDISED TO SNP181
Data processing CHP files were generated using the Affymetrix Genotyping Console algorithm Birdseed v2. Total and allele-specific copy number analysis was performed using Partek Genomics Suite 6.5, using both paired copy number generation.
Submission date Jul 09, 2014
Last update date Mar 01, 2015
Contact name Sally Hunter
Organization name Peter MacCallum Cancer Centre
Department Research
Lab Cancer Genetics
Street address 7 St Andrew's Pl
City Melbourne
State/province VIC
ZIP/Postal code 3002
Country Australia
Platform ID GPL6801
Series (1)
GSE58579 High-resolution genome-wide copy number analysis of low grade serous ovarian tumours

Data table header descriptions
VALUE SNP6 normalized copy number data

Data table
AFFX-SNP_10000979 1.52812
AFFX-SNP_10009702 2.05055
AFFX-SNP_10015773 1.56608
AFFX-SNP_10021569 1.29696
AFFX-SNP_10026879 2.0659
AFFX-SNP_10029725 2.31811
AFFX-SNP_10034687 1.11547
AFFX-SNP_10036267 2.09482
AFFX-SNP_10037362 2.33943
AFFX-SNP_10037636 2.16331
AFFX-SNP_10039349 2.00461
AFFX-SNP_10039442 1.91466
AFFX-SNP_10039933 2.65953
AFFX-SNP_10046830 2.05189
AFFX-SNP_10047363 1.72463
AFFX-SNP_10047841 1.84122
AFFX-SNP_10049334 2.55273
AFFX-SNP_10052664 1.65897
AFFX-SNP_10057887 2.00832
AFFX-SNP_10064911 1.60272

Total number of rows: 1855448

Table truncated, full table size 36288 Kbytes.

Supplementary file Size Download File type/resource
GSM1431037_P1805N.CEL.gz 27.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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